Starting phenix.real_space_refine on Sun Apr 5 08:23:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ly2_63500/04_2026/9ly2_63500.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ly2_63500/04_2026/9ly2_63500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ly2_63500/04_2026/9ly2_63500.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ly2_63500/04_2026/9ly2_63500.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ly2_63500/04_2026/9ly2_63500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ly2_63500/04_2026/9ly2_63500.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 45 5.16 5 C 5687 2.51 5 N 1491 2.21 5 O 1639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8867 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2659 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 22, 'TRANS': 311} Chain breaks: 2 Chain: "C" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1551 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 9, 'TRANS': 195} Chain breaks: 1 Chain: "E" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1587 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 11, 'TRANS': 195} Chain breaks: 1 Chain: "L" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 278 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "R" Number of atoms: 2792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2792 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 336} Chain breaks: 5 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ARG:plan': 3, 'TRP:plan': 1, 'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 26 Time building chain proxies: 2.00, per 1000 atoms: 0.23 Number of scatterers: 8867 At special positions: 0 Unit cell: (82.49, 103.66, 204.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 P 5 15.00 O 1639 8.00 N 1491 7.00 C 5687 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 81 " - pdb=" SG CYS R 397 " distance=1.79 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 99 " distance=2.03 Simple disulfide: pdb=" SG CYS C 150 " - pdb=" SG CYS C 206 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 195 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 311.1 milliseconds 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2122 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 14 sheets defined 29.7% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'B' and resid 44 through 49 Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 98 through 109 Processing helix chain 'B' and resid 278 through 282 removed outlier: 3.889A pdb=" N ARG B 282 " --> pdb=" O CYS B 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 94 Processing helix chain 'C' and resid 166 through 168 No H-bonds generated for 'chain 'C' and resid 166 through 168' Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.950A pdb=" N PHE E 84 " --> pdb=" O PRO E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 128 removed outlier: 3.501A pdb=" N SER E 128 " --> pdb=" O SER E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 190 Processing helix chain 'L' and resid 2 through 33 Processing helix chain 'R' and resid 33 through 55 Processing helix chain 'R' and resid 173 through 176 Processing helix chain 'R' and resid 177 through 212 removed outlier: 3.752A pdb=" N ARG R 181 " --> pdb=" O GLU R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 245 Processing helix chain 'R' and resid 277 through 311 removed outlier: 4.205A pdb=" N CYS R 281 " --> pdb=" O GLY R 277 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 347 removed outlier: 3.541A pdb=" N TYR R 320 " --> pdb=" O SER R 316 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TRP R 322 " --> pdb=" O LYS R 318 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR R 325 " --> pdb=" O LEU R 321 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU R 331 " --> pdb=" O PHE R 327 " (cutoff:3.500A) Proline residue: R 332 - end of helix Processing helix chain 'R' and resid 358 through 387 removed outlier: 4.145A pdb=" N ILE R 362 " --> pdb=" O ASN R 358 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE R 363 " --> pdb=" O LYS R 359 " (cutoff:3.500A) Proline residue: R 366 - end of helix Processing helix chain 'R' and resid 403 through 418 Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 419 through 425 removed outlier: 3.527A pdb=" N MET R 425 " --> pdb=" O ILE R 422 " (cutoff:3.500A) Processing helix chain 'R' and resid 436 through 460 removed outlier: 4.331A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 471 removed outlier: 3.707A pdb=" N LYS R 471 " --> pdb=" O GLN R 467 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 113 through 117 removed outlier: 4.100A pdb=" N VAL B 8 " --> pdb=" O SEP R 523 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SEP R 523 " --> pdb=" O VAL B 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.849A pdb=" N TYR B 144 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LYS B 170 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 9.782A pdb=" N VAL B 142 " --> pdb=" O LYS B 170 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL B 53 " --> pdb=" O GLN B 85 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLN B 85 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL B 55 " --> pdb=" O ASN B 83 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ASN B 83 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU B 57 " --> pdb=" O CYS B 81 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N CYS B 81 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N CYS B 59 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 127 through 129 Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 186 Processing sheet with id=AA5, first strand: chain 'B' and resid 207 through 208 removed outlier: 4.138A pdb=" N TYR B 321 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N LEU B 351 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 9.308A pdb=" N VAL B 319 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL B 328 " --> pdb=" O LYS B 230 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS B 230 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE B 231 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLU B 257 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE B 233 " --> pdb=" O MET B 255 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N MET B 255 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL B 235 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 241 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 9 through 10 removed outlier: 3.534A pdb=" N LEU C 23 " --> pdb=" O LEU C 84 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 14 through 15 removed outlier: 8.326A pdb=" N SER C 35 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N SER C 55 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE C 37 " --> pdb=" O SER C 53 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER C 53 " --> pdb=" O ILE C 37 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TRP C 39 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 130 through 134 removed outlier: 3.551A pdb=" N GLY C 149 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TYR C 186 " --> pdb=" O ASP C 154 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 161 through 164 removed outlier: 3.715A pdb=" N VAL C 217 " --> pdb=" O VAL C 208 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 5 through 7 removed outlier: 5.919A pdb=" N VAL E 20 " --> pdb=" O ILE E 76 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 14 removed outlier: 6.670A pdb=" N VAL E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N TYR E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 11 through 14 removed outlier: 3.584A pdb=" N GLN E 91 " --> pdb=" O THR E 98 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N THR E 98 " --> pdb=" O GLN E 91 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 117 through 119 removed outlier: 3.608A pdb=" N VAL E 134 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LEU E 176 " --> pdb=" O LEU E 137 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN E 139 " --> pdb=" O TYR E 174 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N TYR E 174 " --> pdb=" O ASN E 139 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER E 175 " --> pdb=" O THR E 165 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 147 through 151 removed outlier: 3.546A pdb=" N CYS E 195 " --> pdb=" O LYS E 208 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS E 208 " --> pdb=" O CYS E 195 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL E 206 " --> pdb=" O VAL E 197 " (cutoff:3.500A) 425 hydrogen bonds defined for protein. 1158 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.57 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1387 1.27 - 1.40: 2329 1.40 - 1.54: 5152 1.54 - 1.67: 143 1.67 - 1.81: 60 Bond restraints: 9071 Sorted by residual: bond pdb=" C PHE R 311 " pdb=" O PHE R 311 " ideal model delta sigma weight residual 1.234 1.130 0.104 1.00e-02 1.00e+04 1.08e+02 bond pdb=" OG1 TPO R 519 " pdb=" P TPO R 519 " ideal model delta sigma weight residual 1.717 1.619 0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" OG1 TPO R 520 " pdb=" P TPO R 520 " ideal model delta sigma weight residual 1.717 1.619 0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" O2P TPO R 519 " pdb=" P TPO R 519 " ideal model delta sigma weight residual 1.528 1.613 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" O2P TPO R 520 " pdb=" P TPO R 520 " ideal model delta sigma weight residual 1.528 1.612 -0.084 2.00e-02 2.50e+03 1.77e+01 ... (remaining 9066 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 12186 2.69 - 5.37: 100 5.37 - 8.06: 22 8.06 - 10.74: 3 10.74 - 13.43: 1 Bond angle restraints: 12312 Sorted by residual: angle pdb=" O PHE R 311 " pdb=" C PHE R 311 " pdb=" N MET R 312 " ideal model delta sigma weight residual 121.78 108.35 13.43 1.31e+00 5.83e-01 1.05e+02 angle pdb=" CA PHE B 244 " pdb=" C PHE B 244 " pdb=" N ASN B 245 " ideal model delta sigma weight residual 119.63 115.61 4.02 8.10e-01 1.52e+00 2.47e+01 angle pdb=" C VAL R 432 " pdb=" N SER R 433 " pdb=" CA SER R 433 " ideal model delta sigma weight residual 122.77 116.48 6.29 1.33e+00 5.65e-01 2.24e+01 angle pdb=" N ASN B 223 " pdb=" CA ASN B 223 " pdb=" C ASN B 223 " ideal model delta sigma weight residual 113.50 105.69 7.81 1.65e+00 3.67e-01 2.24e+01 angle pdb=" N THR R 435 " pdb=" CA THR R 435 " pdb=" C THR R 435 " ideal model delta sigma weight residual 111.28 106.13 5.15 1.09e+00 8.42e-01 2.23e+01 ... (remaining 12307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 5143 16.16 - 32.33: 207 32.33 - 48.49: 44 48.49 - 64.65: 6 64.65 - 80.81: 2 Dihedral angle restraints: 5402 sinusoidal: 2113 harmonic: 3289 Sorted by residual: dihedral pdb=" CB CYS B 81 " pdb=" SG CYS B 81 " pdb=" SG CYS R 397 " pdb=" CB CYS R 397 " ideal model delta sinusoidal sigma weight residual -86.00 -120.95 34.95 1 1.00e+01 1.00e-02 1.73e+01 dihedral pdb=" C PHE R 311 " pdb=" N PHE R 311 " pdb=" CA PHE R 311 " pdb=" CB PHE R 311 " ideal model delta harmonic sigma weight residual -122.60 -113.58 -9.02 0 2.50e+00 1.60e-01 1.30e+01 dihedral pdb=" CA ILE R 458 " pdb=" C ILE R 458 " pdb=" N TYR R 459 " pdb=" CA TYR R 459 " ideal model delta harmonic sigma weight residual -180.00 -164.25 -15.75 0 5.00e+00 4.00e-02 9.92e+00 ... (remaining 5399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1216 0.062 - 0.124: 169 0.124 - 0.186: 10 0.186 - 0.248: 1 0.248 - 0.310: 1 Chirality restraints: 1397 Sorted by residual: chirality pdb=" CA PHE R 311 " pdb=" N PHE R 311 " pdb=" C PHE R 311 " pdb=" CB PHE R 311 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA ILE R 310 " pdb=" N ILE R 310 " pdb=" C ILE R 310 " pdb=" CB ILE R 310 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.70e-01 chirality pdb=" CA VAL B 220 " pdb=" N VAL B 220 " pdb=" C VAL B 220 " pdb=" CB VAL B 220 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.58e-01 ... (remaining 1394 not shown) Planarity restraints: 1535 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE R 311 " 0.080 2.00e-02 2.50e+03 1.57e-01 2.47e+02 pdb=" C PHE R 311 " -0.271 2.00e-02 2.50e+03 pdb=" O PHE R 311 " 0.111 2.00e-02 2.50e+03 pdb=" N MET R 312 " 0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 310 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C ILE R 310 " -0.064 2.00e-02 2.50e+03 pdb=" O ILE R 310 " 0.024 2.00e-02 2.50e+03 pdb=" N PHE R 311 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 309 " 0.018 2.00e-02 2.50e+03 3.50e-02 1.22e+01 pdb=" C LEU R 309 " -0.060 2.00e-02 2.50e+03 pdb=" O LEU R 309 " 0.023 2.00e-02 2.50e+03 pdb=" N ILE R 310 " 0.020 2.00e-02 2.50e+03 ... (remaining 1532 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1815 2.78 - 3.31: 8377 3.31 - 3.84: 14366 3.84 - 4.37: 16473 4.37 - 4.90: 28943 Nonbonded interactions: 69974 Sorted by model distance: nonbonded pdb=" O ALA B 263 " pdb=" OG SER B 266 " model vdw 2.253 3.040 nonbonded pdb=" OE1 GLN C 181 " pdb=" OG SER C 187 " model vdw 2.272 3.040 nonbonded pdb=" O LEU R 215 " pdb=" ND2 ASN R 220 " model vdw 2.286 3.120 nonbonded pdb=" OG1 THR E 23 " pdb=" OD1 ASP E 71 " model vdw 2.291 3.040 nonbonded pdb=" O PRO B 124 " pdb=" OH TYR B 144 " model vdw 2.298 3.040 ... (remaining 69969 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 5.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 9.280 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.243 9077 Z= 0.293 Angle : 0.800 36.149 12324 Z= 0.448 Chirality : 0.043 0.310 1397 Planarity : 0.005 0.157 1535 Dihedral : 9.308 80.814 3262 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.55 % Allowed : 3.95 % Favored : 95.50 % Rotamer: Outliers : 1.34 % Allowed : 5.45 % Favored : 93.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.26), residues: 1088 helix: 2.24 (0.31), residues: 283 sheet: 1.54 (0.30), residues: 319 loop : -0.33 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 285 TYR 0.024 0.001 TYR R 191 PHE 0.020 0.001 PHE R 311 TRP 0.006 0.001 TRP R 437 HIS 0.002 0.000 HIS L 32 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 9071) covalent geometry : angle 0.65483 (12312) SS BOND : bond 0.09927 ( 6) SS BOND : angle 14.76880 ( 12) hydrogen bonds : bond 0.19099 ( 420) hydrogen bonds : angle 6.83454 ( 1158) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 248 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 242 CYS cc_start: 0.7621 (t) cc_final: 0.6386 (m) REVERT: C 132 PHE cc_start: 0.7386 (m-80) cc_final: 0.7154 (m-80) REVERT: C 164 TRP cc_start: 0.7757 (m100) cc_final: 0.7437 (m100) REVERT: C 179 VAL cc_start: 0.8590 (t) cc_final: 0.8383 (p) REVERT: E 66 SER cc_start: 0.8093 (t) cc_final: 0.7839 (m) REVERT: E 80 GLN cc_start: 0.7023 (mm110) cc_final: 0.6795 (mm110) REVERT: E 93 LYS cc_start: 0.8223 (tttt) cc_final: 0.7910 (ttpp) REVERT: E 179 THR cc_start: 0.8106 (p) cc_final: 0.7878 (t) REVERT: R 36 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6917 (mm-30) REVERT: R 185 ASP cc_start: 0.7666 (t0) cc_final: 0.7252 (m-30) REVERT: R 282 ARG cc_start: 0.5470 (tmt170) cc_final: 0.5122 (ttt180) REVERT: R 314 PHE cc_start: 0.1401 (OUTLIER) cc_final: -0.0557 (m-80) REVERT: R 424 PHE cc_start: 0.7218 (m-80) cc_final: 0.7005 (m-10) REVERT: R 437 TRP cc_start: 0.7318 (t60) cc_final: 0.6886 (t60) REVERT: R 463 ASN cc_start: 0.7396 (t0) cc_final: 0.7126 (t0) outliers start: 13 outliers final: 2 residues processed: 253 average time/residue: 0.1220 time to fit residues: 39.2723 Evaluate side-chains 150 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 147 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 314 PHE Chi-restraints excluded: chain R residue 433 SER Chi-restraints excluded: chain R residue 436 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.0980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.0270 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.4040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN B 222 ASN B 223 ASN C 31 ASN C 207 ASN E 80 GLN E 148 GLN E 161 GLN R 37 GLN R 358 ASN R 448 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.160341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.122646 restraints weight = 17818.396| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 4.16 r_work: 0.3564 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9077 Z= 0.134 Angle : 0.604 7.821 12324 Z= 0.309 Chirality : 0.043 0.214 1397 Planarity : 0.004 0.040 1535 Dihedral : 4.231 46.640 1235 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.31 % Favored : 96.32 % Rotamer: Outliers : 2.06 % Allowed : 11.63 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.26), residues: 1088 helix: 1.94 (0.30), residues: 294 sheet: 1.55 (0.29), residues: 316 loop : -0.45 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 20 TYR 0.022 0.001 TYR R 191 PHE 0.034 0.002 PHE R 375 TRP 0.010 0.001 TRP R 437 HIS 0.004 0.001 HIS B 353 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9071) covalent geometry : angle 0.60342 (12312) SS BOND : bond 0.00261 ( 6) SS BOND : angle 0.86515 ( 12) hydrogen bonds : bond 0.04291 ( 420) hydrogen bonds : angle 5.04702 ( 1158) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 LYS cc_start: 0.7741 (pttt) cc_final: 0.7291 (pttm) REVERT: B 242 CYS cc_start: 0.7950 (t) cc_final: 0.6697 (m) REVERT: B 285 ARG cc_start: 0.7410 (tpt-90) cc_final: 0.7193 (ttt90) REVERT: C 132 PHE cc_start: 0.7362 (m-80) cc_final: 0.7094 (m-80) REVERT: C 151 LEU cc_start: 0.6664 (tp) cc_final: 0.6432 (tt) REVERT: C 164 TRP cc_start: 0.7642 (m100) cc_final: 0.7336 (m100) REVERT: E 66 SER cc_start: 0.8326 (t) cc_final: 0.8068 (p) REVERT: E 93 LYS cc_start: 0.8443 (tttt) cc_final: 0.7991 (ttpp) REVERT: R 34 LYS cc_start: 0.7530 (ttpp) cc_final: 0.7290 (tttt) REVERT: R 282 ARG cc_start: 0.5438 (tmt170) cc_final: 0.4747 (tmt170) REVERT: R 424 PHE cc_start: 0.7490 (m-80) cc_final: 0.7248 (m-10) REVERT: R 459 TYR cc_start: 0.7802 (m-10) cc_final: 0.7595 (m-10) outliers start: 20 outliers final: 14 residues processed: 168 average time/residue: 0.1154 time to fit residues: 25.4573 Evaluate side-chains 140 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 229 SER Chi-restraints excluded: chain R residue 320 TYR Chi-restraints excluded: chain R residue 326 VAL Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 436 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 28 optimal weight: 0.0470 chunk 42 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 ASN C 207 ASN E 38 GLN E 138 ASN L 10 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.154334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.114768 restraints weight = 17501.970| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 4.28 r_work: 0.3429 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9077 Z= 0.229 Angle : 0.662 7.567 12324 Z= 0.335 Chirality : 0.045 0.262 1397 Planarity : 0.005 0.053 1535 Dihedral : 4.471 28.348 1232 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.86 % Favored : 95.77 % Rotamer: Outliers : 3.09 % Allowed : 12.14 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.26), residues: 1088 helix: 1.69 (0.30), residues: 288 sheet: 1.29 (0.29), residues: 341 loop : -0.53 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 109 TYR 0.021 0.002 TYR C 57 PHE 0.024 0.002 PHE B 277 TRP 0.013 0.002 TRP C 113 HIS 0.009 0.002 HIS B 353 Details of bonding type rmsd covalent geometry : bond 0.00535 ( 9071) covalent geometry : angle 0.66173 (12312) SS BOND : bond 0.00230 ( 6) SS BOND : angle 1.04320 ( 12) hydrogen bonds : bond 0.04297 ( 420) hydrogen bonds : angle 5.00246 ( 1158) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 106 LYS cc_start: 0.7733 (pttt) cc_final: 0.7229 (pttm) REVERT: B 113 TYR cc_start: 0.7536 (m-80) cc_final: 0.7301 (m-80) REVERT: B 223 ASN cc_start: 0.7872 (OUTLIER) cc_final: 0.7184 (t0) REVERT: B 242 CYS cc_start: 0.8090 (t) cc_final: 0.6782 (m) REVERT: C 127 LYS cc_start: 0.7027 (tmtt) cc_final: 0.6807 (tmtt) REVERT: C 132 PHE cc_start: 0.7331 (m-80) cc_final: 0.7016 (m-80) REVERT: C 151 LEU cc_start: 0.6670 (tp) cc_final: 0.6438 (tt) REVERT: C 164 TRP cc_start: 0.7538 (m100) cc_final: 0.7271 (m100) REVERT: E 66 SER cc_start: 0.8560 (t) cc_final: 0.8228 (p) REVERT: E 93 LYS cc_start: 0.8548 (tttt) cc_final: 0.8075 (ttpp) REVERT: L 21 ARG cc_start: 0.6086 (ttm-80) cc_final: 0.5844 (mtt180) REVERT: R 34 LYS cc_start: 0.7531 (ttpp) cc_final: 0.7165 (tttt) REVERT: R 282 ARG cc_start: 0.5378 (tmt170) cc_final: 0.4380 (ttt180) REVERT: R 412 VAL cc_start: 0.6621 (t) cc_final: 0.6337 (t) outliers start: 30 outliers final: 21 residues processed: 158 average time/residue: 0.1169 time to fit residues: 24.4114 Evaluate side-chains 142 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 198 HIS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 229 SER Chi-restraints excluded: chain R residue 316 SER Chi-restraints excluded: chain R residue 320 TYR Chi-restraints excluded: chain R residue 326 VAL Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 436 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 GLN E 138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.154748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.111263 restraints weight = 17755.516| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 3.63 r_work: 0.3498 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9077 Z= 0.155 Angle : 0.600 7.593 12324 Z= 0.304 Chirality : 0.043 0.221 1397 Planarity : 0.004 0.039 1535 Dihedral : 4.382 26.853 1232 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.95 % Favored : 95.68 % Rotamer: Outliers : 2.47 % Allowed : 13.07 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.26), residues: 1088 helix: 1.65 (0.30), residues: 285 sheet: 1.29 (0.28), residues: 341 loop : -0.52 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 65 TYR 0.036 0.002 TYR R 191 PHE 0.021 0.002 PHE B 115 TRP 0.009 0.001 TRP C 113 HIS 0.005 0.001 HIS B 353 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 9071) covalent geometry : angle 0.60032 (12312) SS BOND : bond 0.00143 ( 6) SS BOND : angle 0.74018 ( 12) hydrogen bonds : bond 0.03913 ( 420) hydrogen bonds : angle 4.83204 ( 1158) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 113 TYR cc_start: 0.7442 (m-80) cc_final: 0.7222 (m-80) REVERT: B 242 CYS cc_start: 0.8003 (t) cc_final: 0.6761 (m) REVERT: B 285 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8241 (ttt-90) REVERT: C 127 LYS cc_start: 0.7118 (tmtt) cc_final: 0.6870 (tmtt) REVERT: C 132 PHE cc_start: 0.7342 (m-80) cc_final: 0.7021 (m-80) REVERT: C 151 LEU cc_start: 0.6732 (tp) cc_final: 0.6515 (tt) REVERT: C 164 TRP cc_start: 0.7551 (m100) cc_final: 0.7323 (m100) REVERT: E 66 SER cc_start: 0.8484 (t) cc_final: 0.8151 (p) REVERT: E 93 LYS cc_start: 0.8522 (tttt) cc_final: 0.8050 (ttpp) REVERT: E 166 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7765 (pm20) REVERT: L 21 ARG cc_start: 0.6124 (ttm-80) cc_final: 0.5878 (mtt180) REVERT: R 233 ARG cc_start: 0.7646 (ttt180) cc_final: 0.7294 (ttt180) REVERT: R 282 ARG cc_start: 0.5446 (tmt170) cc_final: 0.4496 (ttt180) REVERT: R 412 VAL cc_start: 0.6682 (t) cc_final: 0.6370 (t) outliers start: 24 outliers final: 17 residues processed: 146 average time/residue: 0.1061 time to fit residues: 20.8863 Evaluate side-chains 143 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 285 ARG Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 229 SER Chi-restraints excluded: chain R residue 316 SER Chi-restraints excluded: chain R residue 320 TYR Chi-restraints excluded: chain R residue 326 VAL Chi-restraints excluded: chain R residue 379 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 52 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 101 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 90 optimal weight: 8.9990 chunk 62 optimal weight: 0.0370 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.154390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.116263 restraints weight = 17547.508| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 3.65 r_work: 0.3478 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9077 Z= 0.149 Angle : 0.583 8.000 12324 Z= 0.295 Chirality : 0.042 0.148 1397 Planarity : 0.004 0.036 1535 Dihedral : 4.302 25.226 1230 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.23 % Favored : 95.40 % Rotamer: Outliers : 3.40 % Allowed : 13.58 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.26), residues: 1088 helix: 1.62 (0.30), residues: 285 sheet: 1.16 (0.28), residues: 342 loop : -0.53 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 11 TYR 0.028 0.002 TYR R 191 PHE 0.026 0.002 PHE B 268 TRP 0.011 0.001 TRP R 329 HIS 0.005 0.001 HIS B 353 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9071) covalent geometry : angle 0.58294 (12312) SS BOND : bond 0.00154 ( 6) SS BOND : angle 0.71728 ( 12) hydrogen bonds : bond 0.03867 ( 420) hydrogen bonds : angle 4.70223 ( 1158) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 TYR cc_start: 0.7474 (m-80) cc_final: 0.7262 (m-80) REVERT: B 223 ASN cc_start: 0.7730 (OUTLIER) cc_final: 0.7147 (t0) REVERT: B 242 CYS cc_start: 0.7969 (t) cc_final: 0.6804 (m) REVERT: B 284 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7776 (ttmt) REVERT: B 285 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8450 (ttt-90) REVERT: C 132 PHE cc_start: 0.7337 (m-80) cc_final: 0.7012 (m-80) REVERT: C 151 LEU cc_start: 0.6864 (tp) cc_final: 0.6658 (tt) REVERT: E 66 SER cc_start: 0.8462 (t) cc_final: 0.8148 (p) REVERT: E 93 LYS cc_start: 0.8506 (tttt) cc_final: 0.8050 (ttpp) REVERT: E 166 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7745 (pm20) REVERT: R 233 ARG cc_start: 0.7778 (ttt180) cc_final: 0.7368 (ttt180) REVERT: R 282 ARG cc_start: 0.5554 (tmt170) cc_final: 0.4541 (ttt180) REVERT: R 412 VAL cc_start: 0.6761 (t) cc_final: 0.6442 (t) REVERT: R 420 HIS cc_start: 0.7144 (p-80) cc_final: 0.6712 (p-80) outliers start: 33 outliers final: 22 residues processed: 161 average time/residue: 0.1133 time to fit residues: 24.1659 Evaluate side-chains 155 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 285 ARG Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 229 SER Chi-restraints excluded: chain R residue 316 SER Chi-restraints excluded: chain R residue 320 TYR Chi-restraints excluded: chain R residue 326 VAL Chi-restraints excluded: chain R residue 379 ILE Chi-restraints excluded: chain R residue 411 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 48 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 62 optimal weight: 0.0070 chunk 25 optimal weight: 4.9990 overall best weight: 0.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.153654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.107884 restraints weight = 17562.221| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 3.11 r_work: 0.3500 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9077 Z= 0.168 Angle : 0.598 7.599 12324 Z= 0.304 Chirality : 0.042 0.148 1397 Planarity : 0.004 0.036 1535 Dihedral : 4.344 26.679 1230 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.50 % Favored : 95.13 % Rotamer: Outliers : 3.29 % Allowed : 14.61 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.26), residues: 1088 helix: 1.71 (0.30), residues: 285 sheet: 1.03 (0.28), residues: 348 loop : -0.52 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 21 TYR 0.026 0.002 TYR R 191 PHE 0.025 0.002 PHE R 375 TRP 0.009 0.001 TRP R 329 HIS 0.005 0.001 HIS B 353 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 9071) covalent geometry : angle 0.59829 (12312) SS BOND : bond 0.00178 ( 6) SS BOND : angle 0.71324 ( 12) hydrogen bonds : bond 0.03862 ( 420) hydrogen bonds : angle 4.69069 ( 1158) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 65 ARG cc_start: 0.7712 (ptt90) cc_final: 0.7445 (ptt90) REVERT: B 106 LYS cc_start: 0.7617 (pttp) cc_final: 0.7256 (pttm) REVERT: B 113 TYR cc_start: 0.7391 (m-80) cc_final: 0.7164 (m-80) REVERT: B 223 ASN cc_start: 0.7762 (OUTLIER) cc_final: 0.7115 (t0) REVERT: B 242 CYS cc_start: 0.7953 (t) cc_final: 0.6773 (m) REVERT: B 285 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8517 (ttt-90) REVERT: C 132 PHE cc_start: 0.7358 (m-80) cc_final: 0.7074 (m-80) REVERT: C 164 TRP cc_start: 0.7757 (m100) cc_final: 0.7477 (m100) REVERT: E 66 SER cc_start: 0.8437 (t) cc_final: 0.8118 (p) REVERT: E 93 LYS cc_start: 0.8499 (tttt) cc_final: 0.8040 (ttpp) REVERT: E 166 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7785 (pm20) REVERT: R 34 LYS cc_start: 0.7603 (ttpp) cc_final: 0.7204 (tttt) REVERT: R 233 ARG cc_start: 0.7673 (ttt180) cc_final: 0.7320 (ttt180) REVERT: R 282 ARG cc_start: 0.5493 (tmt170) cc_final: 0.4571 (ttt180) REVERT: R 312 MET cc_start: 0.5229 (OUTLIER) cc_final: 0.3281 (tpt) REVERT: R 412 VAL cc_start: 0.6786 (t) cc_final: 0.6475 (t) outliers start: 32 outliers final: 24 residues processed: 152 average time/residue: 0.1154 time to fit residues: 23.1719 Evaluate side-chains 153 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 198 HIS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 285 ARG Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 229 SER Chi-restraints excluded: chain R residue 312 MET Chi-restraints excluded: chain R residue 316 SER Chi-restraints excluded: chain R residue 320 TYR Chi-restraints excluded: chain R residue 326 VAL Chi-restraints excluded: chain R residue 379 ILE Chi-restraints excluded: chain R residue 411 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 69 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 7 optimal weight: 0.0370 chunk 94 optimal weight: 0.9980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.153950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.110752 restraints weight = 17588.367| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 3.75 r_work: 0.3468 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9077 Z= 0.139 Angle : 0.579 8.250 12324 Z= 0.293 Chirality : 0.042 0.144 1397 Planarity : 0.004 0.034 1535 Dihedral : 4.282 28.336 1230 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.14 % Favored : 95.50 % Rotamer: Outliers : 2.78 % Allowed : 15.64 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.26), residues: 1088 helix: 1.73 (0.30), residues: 285 sheet: 1.04 (0.28), residues: 344 loop : -0.51 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 21 TYR 0.024 0.002 TYR R 191 PHE 0.018 0.002 PHE C 105 TRP 0.009 0.001 TRP R 298 HIS 0.004 0.001 HIS B 353 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9071) covalent geometry : angle 0.57939 (12312) SS BOND : bond 0.00175 ( 6) SS BOND : angle 0.63149 ( 12) hydrogen bonds : bond 0.03748 ( 420) hydrogen bonds : angle 4.59937 ( 1158) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 113 TYR cc_start: 0.7465 (m-80) cc_final: 0.7227 (m-80) REVERT: B 130 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7130 (tt0) REVERT: B 242 CYS cc_start: 0.7964 (t) cc_final: 0.6963 (m) REVERT: B 285 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8478 (ttt-90) REVERT: C 164 TRP cc_start: 0.7654 (m100) cc_final: 0.7419 (m100) REVERT: E 66 SER cc_start: 0.8433 (t) cc_final: 0.8112 (p) REVERT: E 93 LYS cc_start: 0.8501 (tttt) cc_final: 0.8056 (ttpp) REVERT: E 166 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7741 (pm20) REVERT: L 21 ARG cc_start: 0.6376 (ttm-80) cc_final: 0.6168 (mtt-85) REVERT: R 34 LYS cc_start: 0.7419 (ttpp) cc_final: 0.7189 (tttt) REVERT: R 233 ARG cc_start: 0.7682 (ttt180) cc_final: 0.7338 (ttt180) REVERT: R 282 ARG cc_start: 0.5460 (tmt170) cc_final: 0.4560 (tmt170) REVERT: R 312 MET cc_start: 0.5258 (OUTLIER) cc_final: 0.3243 (tpt) REVERT: R 412 VAL cc_start: 0.6834 (t) cc_final: 0.6531 (t) REVERT: R 441 MET cc_start: 0.5736 (mmt) cc_final: 0.5454 (mmt) outliers start: 27 outliers final: 21 residues processed: 148 average time/residue: 0.1200 time to fit residues: 23.4080 Evaluate side-chains 151 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 285 ARG Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 229 SER Chi-restraints excluded: chain R residue 312 MET Chi-restraints excluded: chain R residue 316 SER Chi-restraints excluded: chain R residue 320 TYR Chi-restraints excluded: chain R residue 326 VAL Chi-restraints excluded: chain R residue 379 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 72 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 56 optimal weight: 0.3980 chunk 8 optimal weight: 0.2980 chunk 55 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.154318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.111193 restraints weight = 17581.742| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 3.50 r_work: 0.3488 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9077 Z= 0.136 Angle : 0.583 9.244 12324 Z= 0.294 Chirality : 0.042 0.143 1397 Planarity : 0.004 0.034 1535 Dihedral : 4.223 29.513 1230 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.32 % Favored : 95.31 % Rotamer: Outliers : 2.78 % Allowed : 15.84 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.26), residues: 1088 helix: 1.82 (0.30), residues: 279 sheet: 1.02 (0.28), residues: 333 loop : -0.47 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 11 TYR 0.022 0.001 TYR R 191 PHE 0.017 0.002 PHE C 105 TRP 0.009 0.001 TRP R 298 HIS 0.007 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9071) covalent geometry : angle 0.58250 (12312) SS BOND : bond 0.00200 ( 6) SS BOND : angle 0.63285 ( 12) hydrogen bonds : bond 0.03700 ( 420) hydrogen bonds : angle 4.52198 ( 1158) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 113 TYR cc_start: 0.7434 (m-80) cc_final: 0.7220 (m-80) REVERT: B 130 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7143 (tt0) REVERT: B 223 ASN cc_start: 0.7855 (OUTLIER) cc_final: 0.7329 (t0) REVERT: B 242 CYS cc_start: 0.7927 (t) cc_final: 0.6956 (m) REVERT: B 285 ARG cc_start: 0.8805 (ttt-90) cc_final: 0.8490 (ttt-90) REVERT: C 180 LEU cc_start: 0.8438 (mm) cc_final: 0.8209 (tp) REVERT: E 66 SER cc_start: 0.8374 (t) cc_final: 0.8056 (p) REVERT: E 93 LYS cc_start: 0.8501 (tttt) cc_final: 0.8070 (ttpp) REVERT: E 166 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7707 (pm20) REVERT: R 34 LYS cc_start: 0.7386 (ttpp) cc_final: 0.7163 (tttt) REVERT: R 233 ARG cc_start: 0.7738 (ttt180) cc_final: 0.7348 (ttt180) REVERT: R 282 ARG cc_start: 0.5468 (tmt170) cc_final: 0.4591 (tmt170) REVERT: R 312 MET cc_start: 0.4960 (OUTLIER) cc_final: 0.3001 (tpp) REVERT: R 412 VAL cc_start: 0.6833 (t) cc_final: 0.6512 (t) REVERT: R 441 MET cc_start: 0.5869 (mmt) cc_final: 0.5440 (mmt) REVERT: R 445 MET cc_start: 0.6240 (mmm) cc_final: 0.6000 (mmm) outliers start: 27 outliers final: 20 residues processed: 152 average time/residue: 0.1162 time to fit residues: 23.3401 Evaluate side-chains 149 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 229 SER Chi-restraints excluded: chain R residue 312 MET Chi-restraints excluded: chain R residue 316 SER Chi-restraints excluded: chain R residue 320 TYR Chi-restraints excluded: chain R residue 326 VAL Chi-restraints excluded: chain R residue 379 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 3 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 26 optimal weight: 0.1980 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 ASN E 138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.153766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.110226 restraints weight = 17481.912| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 3.60 r_work: 0.3469 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9077 Z= 0.143 Angle : 0.591 11.689 12324 Z= 0.296 Chirality : 0.042 0.183 1397 Planarity : 0.004 0.034 1535 Dihedral : 4.258 29.945 1230 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.95 % Favored : 95.68 % Rotamer: Outliers : 2.57 % Allowed : 16.26 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.26), residues: 1088 helix: 1.83 (0.30), residues: 279 sheet: 0.99 (0.29), residues: 329 loop : -0.46 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 21 TYR 0.028 0.002 TYR R 136 PHE 0.034 0.002 PHE L 23 TRP 0.054 0.002 TRP C 164 HIS 0.004 0.001 HIS B 353 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9071) covalent geometry : angle 0.59097 (12312) SS BOND : bond 0.00232 ( 6) SS BOND : angle 0.64662 ( 12) hydrogen bonds : bond 0.03728 ( 420) hydrogen bonds : angle 4.52492 ( 1158) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 83 ASN cc_start: 0.8134 (t0) cc_final: 0.7849 (m-40) REVERT: B 113 TYR cc_start: 0.7470 (m-80) cc_final: 0.7242 (m-80) REVERT: B 130 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7156 (tt0) REVERT: B 223 ASN cc_start: 0.7462 (OUTLIER) cc_final: 0.6987 (t0) REVERT: B 242 CYS cc_start: 0.7948 (t) cc_final: 0.6991 (m) REVERT: B 285 ARG cc_start: 0.8824 (ttt-90) cc_final: 0.8512 (ttt-90) REVERT: C 180 LEU cc_start: 0.8446 (mm) cc_final: 0.8214 (tp) REVERT: E 66 SER cc_start: 0.8373 (t) cc_final: 0.8050 (p) REVERT: E 93 LYS cc_start: 0.8516 (tttt) cc_final: 0.8064 (ttpp) REVERT: E 166 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7731 (pm20) REVERT: R 233 ARG cc_start: 0.7751 (ttt180) cc_final: 0.7338 (ttt180) REVERT: R 282 ARG cc_start: 0.5479 (tmt170) cc_final: 0.4613 (tmt170) REVERT: R 412 VAL cc_start: 0.6860 (t) cc_final: 0.6553 (t) outliers start: 25 outliers final: 22 residues processed: 144 average time/residue: 0.1153 time to fit residues: 21.8631 Evaluate side-chains 149 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 229 SER Chi-restraints excluded: chain R residue 316 SER Chi-restraints excluded: chain R residue 320 TYR Chi-restraints excluded: chain R residue 326 VAL Chi-restraints excluded: chain R residue 379 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 48 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 ASN E 4 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.152599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.108625 restraints weight = 17439.753| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 3.67 r_work: 0.3441 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9077 Z= 0.197 Angle : 0.627 8.731 12324 Z= 0.319 Chirality : 0.043 0.151 1397 Planarity : 0.004 0.037 1535 Dihedral : 4.448 29.848 1230 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.60 % Favored : 95.04 % Rotamer: Outliers : 2.67 % Allowed : 16.87 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.26), residues: 1088 helix: 1.72 (0.30), residues: 280 sheet: 0.78 (0.28), residues: 348 loop : -0.41 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 21 TYR 0.024 0.002 TYR R 191 PHE 0.035 0.002 PHE L 23 TRP 0.039 0.002 TRP C 164 HIS 0.005 0.001 HIS B 353 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 9071) covalent geometry : angle 0.62695 (12312) SS BOND : bond 0.00201 ( 6) SS BOND : angle 0.80021 ( 12) hydrogen bonds : bond 0.03924 ( 420) hydrogen bonds : angle 4.63316 ( 1158) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 15 ASN cc_start: 0.6730 (m110) cc_final: 0.6501 (m110) REVERT: B 83 ASN cc_start: 0.8175 (t0) cc_final: 0.7893 (m-40) REVERT: B 113 TYR cc_start: 0.7589 (m-80) cc_final: 0.7328 (m-80) REVERT: B 130 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7067 (tt0) REVERT: B 223 ASN cc_start: 0.7722 (OUTLIER) cc_final: 0.7247 (t0) REVERT: B 242 CYS cc_start: 0.8057 (t) cc_final: 0.7060 (m) REVERT: B 285 ARG cc_start: 0.8840 (ttt-90) cc_final: 0.8541 (ttt-90) REVERT: C 180 LEU cc_start: 0.8500 (mm) cc_final: 0.7994 (tt) REVERT: E 66 SER cc_start: 0.8420 (t) cc_final: 0.8094 (p) REVERT: E 93 LYS cc_start: 0.8579 (tttt) cc_final: 0.8093 (ttpp) REVERT: E 166 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7736 (pm20) REVERT: R 233 ARG cc_start: 0.7776 (ttt180) cc_final: 0.7406 (ttt180) REVERT: R 282 ARG cc_start: 0.5436 (tmt170) cc_final: 0.4565 (tmt170) REVERT: R 312 MET cc_start: 0.4918 (OUTLIER) cc_final: 0.2960 (tpp) REVERT: R 412 VAL cc_start: 0.6923 (t) cc_final: 0.6608 (t) REVERT: R 445 MET cc_start: 0.6256 (mmm) cc_final: 0.6034 (mmm) outliers start: 26 outliers final: 22 residues processed: 145 average time/residue: 0.1202 time to fit residues: 22.7969 Evaluate side-chains 148 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 CYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain L residue 15 ILE Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 229 SER Chi-restraints excluded: chain R residue 312 MET Chi-restraints excluded: chain R residue 316 SER Chi-restraints excluded: chain R residue 320 TYR Chi-restraints excluded: chain R residue 326 VAL Chi-restraints excluded: chain R residue 379 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 0.0020 chunk 2 optimal weight: 0.7980 chunk 98 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 81 optimal weight: 8.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 222 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.153884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.112012 restraints weight = 17432.502| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 3.80 r_work: 0.3482 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9077 Z= 0.127 Angle : 0.591 12.169 12324 Z= 0.295 Chirality : 0.041 0.142 1397 Planarity : 0.004 0.034 1535 Dihedral : 4.317 31.026 1230 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.77 % Favored : 95.86 % Rotamer: Outliers : 2.47 % Allowed : 17.08 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.26), residues: 1088 helix: 1.83 (0.30), residues: 279 sheet: 0.93 (0.28), residues: 334 loop : -0.47 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 161 TYR 0.024 0.001 TYR R 191 PHE 0.034 0.002 PHE L 23 TRP 0.034 0.002 TRP C 164 HIS 0.003 0.001 HIS B 353 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9071) covalent geometry : angle 0.59111 (12312) SS BOND : bond 0.00181 ( 6) SS BOND : angle 0.61911 ( 12) hydrogen bonds : bond 0.03689 ( 420) hydrogen bonds : angle 4.50376 ( 1158) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3018.40 seconds wall clock time: 52 minutes 16.21 seconds (3136.21 seconds total)